SMTL ID : 7p18.1 (1 other biounit)

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Sterolibacterium denitrificans in complex with 1,4-androstadiene-3,17-dione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 35 residues within 4Å: Chain A: V.13, G.14, S.15, G.16, V.36, E.37, K.38, G.43, G.44, T.45, S.46, V.48, S.49, G.50, G.51, A.52, P.232, F.233, G.269, A.270, G.271, A.294, H.298, N.299, D.302, F.338, I.496, G.525, N.526, Y.536, G.540, G.541, T.542, L.543 Ligands: ANB.2 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:T.45, A:A.294, A:F.338, A:F.338, A:I.496, A:I.496 Hydrogen bonds: A:S.15, A:K.38, A:K.38, A:T.45, A:S.46, A:S.46, A:S.49, A:S.49, A:G.50, A:A.52, A:A.52, A:F.233, A:F.233, A:G.271, A:N.299, A:D.302, A:I.496, A:N.526, A:N.526, A:G.540, A:T.542, A:T.542, A:L.543 Water bridges: A:G.16, A:A.17, A:G.18, A:G.18, A:S.39, A:N.299, A:G.301, A:N.527

1 x ANB: ANDROSTA-1,4-DIENE-3,17-DIONE(Non-covalent)

ANB.2: 9 residues within 4Å: Chain A: A.52, Y.115, A.166, F.338, Y.363, Y.536, A.539, G.540 Ligands: FAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.52, A:Y.115, A:A.166, A:F.338, A:F.338, A:F.338, A:A.539 Hydrogen bonds: A:Y.363, A:G.540

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: Q.120, H.121, N.461, V.462 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.461, A:V.462 Water bridges: A:Q.120, A:R.465 PEG.4: 6 residues within 4Å: Chain A: C.112, H.113, R.114, Y.115, T.167, Y.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.114, A:Y.115, A:Y.466 Water bridges: A:H.113 PEG.5: 2 residues within 4Å: Chain A: R.419, Q.429 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.419

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: K.175, E.176, W.179, Q.404 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.175, A:E.176, A:Q.404 Water bridges: A:M.172, A:K.175 GOL.7: 4 residues within 4Å: Chain A: R.25, D.28, Y.100, N.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.25 GOL.8: 5 residues within 4Å: Chain A: R.197, L.198, K.199, S.200, R.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.198, A:R.201

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 2 residues within 4Å: Chain A: R.150, M.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.151 Water bridges: A:M.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wojcik, P. et al., Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Delta 1 -Dehydrogenase from Sterolibacterium denitrificans ─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis. Biochemistry (2023)

Release Date

2021-07-21

Peptides

3-oxosteroid 1-dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-oxosteroid 1-dehydrogenase

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